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BMRB: 18375

2LRJ

NMR solution structure of staphyloxanthin biosynthesis protein

Authors

Zhang, Y., Winsor, J., Anderson, W., Radhakrishnan, I.

Assembly

staphyloxanthin protein

Entity

1. staphyloxanthin protein (polymer, Thiol state: all free), 113 monomers, 11715.48 Da Detail

GSSISHSGNL YTAGQCTWYV YDKVGGEIGS TWGNANNWAA AAQGAGFTVN HTPSKGAILQ SSEGPFGHVA YVESVNSDGS VTISEMNYSG GPFSVSSRTI SASEAGNYNY IHI

Formula weight

11715.48 Da

Source organism

Staphylococcus aureus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 95.1 %, Completeness (bb): 95.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.1 % (1128 of 1186)	96.2 % (575 of 598)	93.5 % (433 of 463)	96.0 % (120 of 125)
Backbone	95.7 % (643 of 672)	95.4 % (228 of 239)	96.0 % (310 of 323)	95.5 % (105 of 110)
Sidechain	94.9 % (580 of 611)	96.7 % (347 of 359)	92.0 % (218 of 237)	100.0 % (15 of 15)
Aromatic	84.8 % (117 of 138)	92.8 % (64 of 69)	75.8 % (50 of 66)	100.0 % (3 of 3)
Methyl	97.1 % (101 of 104)	96.2 % (50 of 52)	98.1 % (51 of 52)

1. entity

GSSISHSGNL YTAGQCTWYV YDKVGGEIGS TWGNANNWAA AAQGAGFTVN HTPSKGAILQ SSEGPFGHVA YVESVNSDGS VTISEMNYSG GPFSVSSRTI SASEAGNYNY IHI

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		137 mM
9	beta-mercaptoethanol	natural abundance		5 mM
10	sodium phosphate	natural abundance		10 mM
11	potassium phosphate	natural abundance		2 mM
12	D2O	natural abundance		100 %
13	staphyloxanthin_protein	natural abundance		0.7 mM

LACS Plot; CA

Referencing offset: -1.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -1.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.31 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LRJ, Strand ID: A Detail

Release date

2012-04-30

Citation

Solution structure of a putative S. aureus enzyme involved in the biosynthesis of staphyloxanthin
Zhang, Y., Winsor, J., Anderson, W., Radhakrishnan, I.
Not known

Related entities 1. staphyloxanthin protein, : 1 : 1 : 26 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

4 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	sodium chloride	natural abundance		137 mM
2	beta-mercaptoethanol	natural abundance		5 mM
3	potassium phosphate	natural abundance		2 mM
4	sodium phosphate	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %
7	staphyloxanthin_protein	natural abundance		0.7 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		137 mM
9	beta-mercaptoethanol	natural abundance		5 mM
10	sodium phosphate	natural abundance		10 mM
11	potassium phosphate	natural abundance		2 mM
12	D2O	natural abundance		100 %
13	staphyloxanthin_protein	natural abundance		0.7 mM

10 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		137 mM
9	beta-mercaptoethanol	natural abundance		5 mM
10	sodium phosphate	natural abundance		10 mM
11	potassium phosphate	natural abundance		2 mM
12	D2O	natural abundance		100 %
13	staphyloxanthin_protein	natural abundance		0.7 mM

11 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		137 mM
9	beta-mercaptoethanol	natural abundance		5 mM
10	sodium phosphate	natural abundance		10 mM
11	potassium phosphate	natural abundance		2 mM
12	D2O	natural abundance		100 %
13	staphyloxanthin_protein	natural abundance		0.7 mM

12 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.8 (±0.1)

#	Name	Isotope labeling	Type	Concentration
8	sodium chloride	natural abundance		137 mM
9	beta-mercaptoethanol	natural abundance		5 mM
10	sodium phosphate	natural abundance		10 mM
11	potassium phosphate	natural abundance		2 mM
12	D2O	natural abundance		100 %
13	staphyloxanthin_protein	natural abundance		0.7 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18375_2lrj.nef
Input source #2: Coordindates	2lrj.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GSSISHSGNLYTAGQCTWYVYDKVGGEIGSTWGNANNWAAAAQGAGFTVNHTPSKGAILQSSEGPFGHVAYVESVNSDGSVTISEMNYSGGPFSVSSRTI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSSISHSGNLYTAGQCTWYVYDKVGGEIGSTWGNANNWAAAAQGAGFTVNHTPSKGAILQSSEGPFGHVAYVESVNSDGSVTISEMNYSGGPFSVSSRTI

-------110---
SASEAGNYNYIHI
|||||||||||||
SASEAGNYNYIHI

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_18375_2lrj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1129		98.2 (chain: A, length: 113)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2666 (1)	noe	98.2 (chain: A, length: 113)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	90 (90)	.	55.8 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 577
  - ¹³C chemical shifts: 433
  - ¹⁵N chemical shifts: 119
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 98.2%
- Total number of restraints: 2657
- Weight of restraints: 1.0 (2657)
- Potential type of restraints: square-well-parabolic (2657)
- Range of distance target values: 1.75, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 55.8%
- Total number of restraints: 90
- Total number of restraints per polymer type: 90
- Weight of restraints: 1.0 (90)
- Potential type of restraints: square-well-parabolic (90)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords biosynthesis, NMR, staphyloxanthin